Are there really 22 genes associated with intelligence?

In a GWAS recently published in Nature Genetics, a team of scientists from around the world analyzed the DNA sequences of 78,308 people for correlations with general intelligence, as measured by IQ tests.

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Of the over 12 million SNPs analyzed, 336 correlated significantly with intelligence, implicating 22 different genes. One of the genes is involved in regulating the growth of neurons; another is associated with intellectual disability and cerebral malformation. Together, the SNPs accounted for about 5% of the differences across people in intelligence—a nearly two-fold increase over the last GWAS on intelligence. Examining larger patterns of SNPs, the researchers discovered an additional 30 genes related to intelligence.

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Of course, intelligence is not solely the product of DNA—and no scientist studying intelligence thinks otherwise. The environment has a major impact on the development of intelligence, or any other psychological trait. More.

Given the disclaimer “intelligence is not solely the product of DNA,” one wonders: If a human being appears to have all his marbles but lacks four of those genes, is he still considered “intelligent”? Isn’t this one of those situations where what happens in real life is what fundamentally matters?

20 Responses to Are there really 22 genes associated with intelligence?

Two important points: look at Table 1, that lists the most significant Genomic loci and lead SNPs associated with intelligence. There are 18 listed. Most of the SNPs are intronic, the rest is intergenic or however non coding.

Talk of junk DNA!

The second point: I have analyzed briefly the evolutionary history of the 4 genes mentioned on page 4 as highly significant in their association (BMPR2, HANK3, DCC and ZFHX3), and the result is: all of them have a very significant information jump in vertebrates.

The most amazing is ZFHX3, a Transcriptional regulator which can act as an activator or a repressor, and which has extremely complex functions in many networks.

GPuccio: I have analyzed briefly the evolutionary history of the 4 genes mentioned on page 4 as highly significant in their association (BMPR2, HANK3, DCC and ZFHX3), and the result is: all of them have a very significant information jump in vertebrates.

Are there good examples of smooth protein transitions between prevertebrates and vertebrates? How usual or unusual is it that we see huge information-jumps between prevertebrates and vertebrates? IOWs are, at this interval, large information-jumps of more than 500 bits the rule or the exception?
Finally, do we see information-jumps, like the 3503 bits related to ZFHX3, only between prevertebrates and vertebrates?

“Are there good examples of smooth protein transitions between prevertebrates and vertebrates? How usual or unusual is it that we see huge information-jumps between prevertebrates and vertebrates?”

Of course. A lot of proteins show no significant jump in that transition.

If you remember that the maximum information content of a protein, using the metrics I have adopted, is little more than 2 baa (bits per aminoacid site), the distribution of the jump in human conserved information, between pre-vertebrates and cartilaginous fish, is the following, for the whole human genome:

Mean jump = 0.28796 baa

Standard deviation = 0.3153395 baa

Median jump = 0.264275 baa

The jump for ZFHX3 id:

0.9459897 baa

and it corresponds approximately to the 97.5 percentile. That means than only 2.5% of human proteins exhibit such a jump, or higher, from pre-vertebrates to vertebrates, in the human genome.

“IOWs are, at this interval, large information-jumps of more than 500 bits the rule or the exception?”

They are the exception, or at least a rather extreme case.

For ZFHX3, we must consider that not only the jump in baa is extremly big, but the protein is also very very long (3703 AAs). That’s why the jump in absolute bits is so big (3503 bits).

In term of absolute bits, the distribution of the jump from pre-vertebrates to vertebrates is as follows:

Mean jump = 189.5817 bits

Standard deviation = 355.6362 bits

Median jump = 99 bits

Our value of 3503 bits here corresponds approximately to the 99.92 percentile, which means that only 0.08% of human proteins present an absolute jump in bits equal to or higher than that. So, in terms of absolute bits, this jump is even more extreme than in terms of baa.

“Finally, do we see information-jumps, like the 3503 bits related to ZFHX3, only between prevertebrates and vertebrates?”

No, we see them also at other point, for example in the transition to mammals. Moreoever, we could explore in a similar way other branches of the evolutionary tree, for example using some other genome as a probe, let’s say apis mellifera genome to explore the evolution of hymenoptera conserved information.

The procedure can be applied impartially to explore different aspects of information development in evolutionary history. I have focused my work on human conserved information and on the transition to vertebrates because that seemed to be a very good model to show how functional information shows huge jumps that can be explained only by design.

Thank you very much for answering my questions. Based on the information you have provided I do not understand what wd400 is saying in this thread.

wd400: The question of finding (or, actually inferring) ancestral intermediates is a strange one. First, such intermediates obviously exist, bacause the proteins are not 100% conserved, allowing us to infer ancestral states.
If you look only at those amino acids are conserved then ask for the intermediates then obviously we won’t find them.

“Obviously we won’t find them”? Based on your answer (“a lot of proteins show no significant jump in that transition.”) in most cases intermediates have already been found.

wd400:It is also strange to ask think discontinuous jumps between clades is a problem and not a prediction of evolution down a tree.

“Discontinuous jumps” are not the rule but the exception, so obviously there is something wrong with evolution’s prediction capability.

wd400: All vertebrates share ~30 million years of evolutionary history, variation that occured in that time are not available for study when we look at modern organisms.

We do see homology for most proteins in modern organisms, so there is little reason for the evolutionist to state that “variation that occured in that time are not available for study when we look at modern organisms.”

Given the disclaimer “intelligence is not solely the product of DNA,” one wonders: If a human being appears to have all his marbles but lacks four of those genes, is he still considered “intelligent”?

I, at least, wonder “why not”? As anyone who has read the quotes in the OP will know, “[t]ogether, the SNPs accounted for about 5% of the differences across people in intelligence”, so they really don’t explain a lot of the variation. IOW the difference between someone with all of the “intelligent” alleles, and someone with the “dumb” alleles is, when all else is equal, not very big.

What’s the officially “acceptable” explanation for the jumps of functional information in the proteins you have analyzed in this and other threads?

What is it that you don’t like in the officially “acceptable” explanation?

Could it be that the officially “acceptable” explanation requires certain level of knowledge in order to be understood well? If somebody lacks the required knowledge, how can one understand the officially “acceptable” explanation?

As you well know, there is no “official”, least of all “acceptable”, explanation for those jumps of functional information. Indeed, nobody would probably acknowledge that those jumps exist, or that they are of any interest.

For the official “theory”, if two proteins show some homology, it’s certain that neo-darwinian evolution did it, even if hundreds or thousands of buts of new functional information have been rather suddenly added in the course of natural history. Who cares? Given that design is impossible for them, neo-darwinian evolution certainly did it in some way? And if you ask what way, you are just asking petty questions, or, as you often say, you just don’t understand evolution.

Well, I certainly don’t understand it! It is probably some genetic hole in my cognitive functions, maybe too many SNPs in those 22 proteins… 🙂

In my dumb ignorance, I cannot even understand what the “required knowledge” could be, and my not brilliant mind can only suggest that the required quality is simply blind faith is a squalid doctrine.

Whence cometh the information? And where the heck is it all stored? In another thread I posed the question:

If most of our genome is junk, then where is the information stored for the (adult) body plan? Where is the information stored for e.g. the brain? And where is the information stored for how to build all this?

Here are the answers by Larry Moran and WD400:

Larry Moran: …. experts do not see a need to encode body plans and brain in our genome …

WD400: If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on.

Eric Anderson summarized their position as follows:

Eric Anderson: … this thread may have uncovered at least one aspect of the simplistic thinking that leads a person to believe that most DNA is junk.
After all, the thinking goes, all we need to do is specify some parts in the DNA and the machine will build itself all by chemistry. It’s easy! No plan needed. No program required. Just specify some gene products and we’re done. Everything else is probably just junk.
Amazing what chemistry can do.

Darwinists are the worst type of reductionists: they will deny complexity with all their strength, simply because complexity means the death of their beloved theory.

The information that guides the epigenetic procedures which build up a multicellular organism remains one of the biggest mysteries in biology: what is it? where is it written? how does it work?

We have no idea.

Darwinists insist that there is no need to have an idea about that. Ideas are, for them, unnecessary luxuries.

I don’t agree. Ideas about reality are one of the treasures of human condition, and I like them.

So, I would really like to know where that information is. Still, it is really elusive, and the more we understand about the infinite details of biological complexity, the more the nature and location of the guiding information seems to defy us.

I will try to suggest a few possible fields of exploration:

a) Information in proteins, especially in regulatory proteins, is hugely underestimated by current biological thoughts. In my recent posts, I have tried to show that there is much more functional information in proteins than is usually believed. Transcription factors, for example, do not work only by their ultra-conserved DNA binding domains, but rather by almost all other aminoacid sites in their sequence. Inter-domain sequences are highly conserved, and functional. And they often differ a lot between different branches of the evolutionary tree. They do very important things, and they do those things differently in different contexts.

Darwinists like to think that great part of the protein sequences is not really necessary to function: that is a tragic mistake, as usual motivated by the need to believe that proteins are simpler than they appear, because even that simplicity is impossible to explain (without design), and the true complexity of them is a nightmare for the theory.

b) Information in non coding DNA is tragically underestimated. This thread proves that SNPs in non coding DNA, introns or intergenic traits, are strongly related to intelligence. We have really no idea of how important introns or intergenic sequences are to the function of the cell.

The world of non coding RNAs is just beginning to be understood.

Let’s be sincere: we have really no idea of how the complex levels of regulatory proteins, regulatory RNAs, regulatory epigenetic layers, and so on, are related, controlled and guided. Where are the basic decisions initiated. Whoever has followed the many links provided by Dionisio in the last few years can get a faint idea of how complex everything is, of how little we understand, even with the amazing advancements of our learning.

c) And still… there is something big missing. Even with all the information in proteins, in non coding DNA, in the epigenome, even getting rid of the lies of darwinists, there is still, IMO, something very big missing. I really don’t know what it is. I can imagine that there can be layers of complex information of which we still have no idea at all, not even in our imagination. Maybe they are hidden in the dark complexities of biophysics, where organic molecules are not static objects, but infinitely complex systems of atoms in continuous change. Maybe they are to be found at the elusive quantum level that is expressed in critical biological processes. Maybe they are something else completely.

I don’t know.

But I agree with you, the information for the brain (and much else) is certainly not just the lucky interaction of a few thousands genes.

GPuccio: The information that guides the epigenetic procedures which build up a multicellular organism remains one of the biggest mysteries in biology: what is it? where is it written? how does it work?

We have no idea.

We have no idea given a naturalistic context, which we may very well need to get rid of.

GPuccio: Darwinists insist that there is no need to have an idea about that. Ideas are, for them, unnecessary luxuries.

Larry Moran, wd400 and kindred spirits have to deny the obvious:

At a construction site, builders will make use of many materials: lumber, wires, nails, drywall, piping, and windows. Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood. Similarly, electronic circuits are composed of many components, such as resistors, capacitors, and transistors. But such lower-level components do not determine their own arrangement in an integrated circuit.
In a similar way, DNA does not by itself direct how individual proteins are assembled into these larger systems or structures—cell types, tissues, organs, and body plans—during animal development. [S.Meyer, ‘Darwin’s Doubt’]

GPuccio: And still… there is something big missing. Even with all the information in proteins, in non coding DNA, in the epigenome, even getting rid of the lies of darwinists, there is still, IMO, something very big missing. I really don’t know what it is. I can imagine that there can be layers of complex information of which we still have no idea at all, not even in our imagination. Maybe they are hidden in the dark complexities of biophysics, where organic molecules are not static objects, but infinitely complex systems of atoms in continuous change. Maybe they are to be found at the elusive quantum level that is expressed in critical biological processes. Maybe they are something else completely.

I don’t know.

There must be a unifying principle at work — a non-material unity which temporarily guides and holds material parts together. A form very similar to consciousness.

gpuccio @15:
“Let’s be sincere: we have really no idea of how the complex levels of regulatory proteins, regulatory RNAs, regulatory epigenetic layers, and so on, are related, controlled and guided. Where are the basic decisions initiated.”